Dear Igor,
On Sat, May 17, 2008 at 1:10 AM, Igor Filippov [Contr]
<ig...@helix.nih.gov> wrote:
>
> I was wondering if you could advise me how to obtain the following
> counts with RDKit:
> - The number of aromatic rings
> - The number of 3,4,5,6,7-member rings
>
> There doesn't seem to be an API function that I can find to get those
> numbers, is it possible to do this with some simple SMARTS patterns?
There's not a single API function to do what you want and I don't
think it would be straightforward to express eiterh as a query. It's
pretty easy to do anyway. From C++ the ring counting looks something
like:
// count the number of rings of size 4:
unsigned int nRingsSize4=0;
for(VECT_INT_VECT_CI ringIt=atomRings.begin();
ringIt!=atomRings.end();++ringIt){
if(ringIt->size()==4) nRingsSize4++;
}
For the aromatic rings (defined to be rings where every bond is aromatic):
unsigned int nAromaticRings=0;
for(VECT_INT_VECT_CI ringIt=bondRings.begin();
ringIt!=bondRings.end();++ringIt){
bool isAromatic=true;
for(INT_VECT_CI bondIt=ringIt->begin();
bondIt!=ringIt->end();++bondIt){
if(!mol->getBondWithIdx(*bondIt)->getIsAromatic()){
isAromatic=false;
break;
}
}
if(isAromatic) nAromaticRings++;
}
Both of these are building on the earlier sample code, which has been
updated in subversion:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/Demos/RDKit/GettingStarted/sample.cpp?view=markup
Note that in each case the symmetrized set of smallest rings is used,
so cubane would give you 6 four membered rings and nothing else.
I hope this helps,
-greg
